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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACACTATTATGAACGGTGGGCAGCCAATCAGTCGgtaagttattgggtacaagaaaagttacctgaacaaagcattgtgttttacataagtagtaaaaaagatttccaatcaatactcaagaagaacttttctggtttcttaatatcttctcgttatgcag

Basic information

species Oryza sativa
transcript LOC_Os04g41470.2
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g41470.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G006428_T02 (Zea mays), 5'ss of exon 10
TATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACACTATTATGAACGGTGGGCAGCCAATCAGTCGgtaagttattgggtacaagaaaagttacctgaacaaagcattgtgttttacataagtagtaaaaaagatttccaatcaatactcaagaagaacttttctggtttcttaatatcttctcgttatgcag
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||| |||||||||||||||||||||||| ||||  |     | || | |||||||     | ||   | | |||||    | |    |||||  ||||  || |     ||| |   |  ||| |                        
TATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACATTATTATGAACGATGGGCAGCCAATCAGTCGgtaagt-attgaatgtggcagaaatgacctgaa----actttaaatct-acatagcatggagttcagattgacaattgatgcatgccaagcatcctgttggctgga---------------------

upper sequence: LOC_Os04g41470.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM5G876621_T01 (Zea mays), 5'ss of exon 10
TATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACACTATTATGAACGGTGGGCAGCCAATCAGTCGgtaagttattgggtacaagaaaagttacctgaacaaagcattgtgttttacataagtagtaaaaaagatttccaatcaatactcaagaagaacttttctggtttcttaatatcttctcgttatgcag
||||||||||||||||||||||||||||||||||||||||| ||||||||||| ||||| ||||||||||| |||||||||||||||||||||||| ||||  |       |||| |||||||      | | |   |||     |   | |   ||| |  ||||  || |     |     | |  |||                          
TATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCCCTTGAGAGATACACACATTATTATGAACGATGGGCAGCCAATCAGTCGgtaagt-attgaatgtggttgaagtgacctgaaacttcaaatctacattagcatggagttcattcagagtgacaattgatgcatgccagctgttctgttgg--------------------------

upper sequence: LOC_Os04g41470.1 (Oryza sativa), 5'ss of exon 10
lower sequence: AT1G65430.1 (Arabidopsis thaliana), 5'ss of exon 10
TATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACACTATTATGAACGGTGGGCAGCCAATCAGTCGgtaagttattgggtacaagaaaagttacctgaacaaagcattgtgttttacataagtagtaaaaaagatttccaatcaatactcaagaagaacttttctggtttcttaatatcttctcgttatgcag
||||||||  ||||||   |  |||| |||||||||||||| |||||||||||||| ||||| |||||  | |||||| ||||||| |||||| || | |   ||           |  |     ||      |||||||  ||  |  |         ||  |    | | | |||||  | |||||  |      |||   |  || |       
TATGATGAGACTGAAAAACGCCGAGAGATGGCAAAGAACTCTCTTGAGAGATATACCCACTACTATGAGAGATGGGCAACCAATCAATCGgtatgtaaatttttat--------ccatttag---aattcacatgttttatttagctcct--------cttgaaggggaaatttaagaaagaattttc-agccgtcaaattcatattcct-------

upper sequence: LOC_Os04g41470.1 (Oryza sativa), 5'ss of exon 10
lower sequence: PP1S9_199V6.1 (Physcomitrella patens), 5'ss of exon 11
TATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACACTATTATGAACGGTGGGCAGCCAATCAGTCGgtaagtt---attgggtacaagaaaagt-------tacctgaacaaagcattgtgttttacataa-gtagtaaaaaagattt--ccaatcaat--actcaagaagaacttttctggtttcttaatatc-ttctcgttatgcag----------
||||||||| | ||  ||||||| |||||||| |||||||| |||||  | || |||||||||||||| || |||||  | ||  | || || |||    ||| |  |      |  |       ||| | |   |   | | | |||  |||||   | || | | |  ||  | |     |  | | ||   ||  ||||      | | ||| |   ||   |  | | |          
TATGATGAAGCAGAGCGGAGAAGGGAAATGGCGAAGAACTCCCTTGAACGTTACACACACTATTATGAGCGTTGGGCTACAAACGAATCTgtgagtactaatttgagatggtgcacttcttccactacgttagttatataatctttttcccataacacactagagatgcattgactacctggttaatttaatgtgatgtttttcatcatttcaatcttactcaaatccttctgatgtgtgcag

upper sequence: LOC_Os04g41470.1 (Oryza sativa), 5'ss of exon 10
lower sequence: PP1S114_2V6.1 (Physcomitrella patens), 5'ss of exon 10
TATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACACTATTATGAACGGTGGGCAGCCAATCAGTCGgtaagttattgggtacaagaaaagtt----acctgaacaaagcattgt---gttttacataag--------tagtaaaaaagatttccaatcaat----actcaagaa---gaact----------tttctggtttcttaatatcttctc-gttatgcag
||||||||| | ||  ||||||| |||||||| ||||||||||||||  | |||||||| || |||||||| |||||  | ||  | || ||||||  |   | |   | | | ||    | |||||  | |  ||     |||   |||  |        || |    | ||| |  | ||  |    | | ||  |   || ||          ||||| |  | || | |||| ||  ||| | |||
TATGATGAAGCAGAGCGGAGAAGGGAAATGGCTAAGAACTCGCTTGAACGCTATACACATTACTATGAACGTTGGGCTACAAACGAATCTgtaagtggtgcagaatctgcacattttcccatctgaattaggttttcctcagttcgccatgggattgcacctattgtttaggatcttaactctctctcaatttaaagacgtgatctgcgtttgtgttttcttgacttttgaaatctcctttgtttttcag

upper sequence: LOC_Os04g41470.1 (Oryza sativa), 5'ss of exon 10
lower sequence: EFJ15174 (Selaginella moellendorffii), 5'ss of exon 10
TATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACACTATTATGAACGGTGGGCAGCCAATCAGTCGgtaagttattgggtacaagaaaagttacctgaacaaagcattgtgttttacataagtagtaaaaaagatttccaatcaatactcaagaagaacttttctggtttcttaatatcttctcgttatgcag
|| |||||| |||| ||||| ||||||||||| ||||||||| | |||||||||||||| || || || || |||||  | ||  | || ||    | |    |   ||      || ||||  |   | || |   || | |   | ||| |                                                                
TACGATGAAGCTGAGAGGAGGAGAGAAATGGCTAAGAACTCGTTAGAGAGATATACACATTACTACGAGCGATGGGCCACGAACGAATCAgttgagtttccaatttgag------tatctga-taggcctttctaactt-cgttcatggtacag---------------------------------------------------------------

upper sequence: LOC_Os04g41470.1 (Oryza sativa), 5'ss of exon 10
lower sequence: EFJ08409 (Selaginella moellendorffii), 5'ss of exon 10
TATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACACTATTATGAACGGTGGGCAGCCAATCAGTCGgtaagttattgggtacaagaaaagttacctgaacaaagcattgtgttttacataagtagtaaaaaagatttccaatcaatactcaagaagaacttttctggtttcttaatatcttctcgttatgcag
|| |||||| |||| ||||| || |||||||| ||||||||| | |||||||||||||| || || || || |||||  | ||  | || ||    | |    |   ||      || ||||  |   | || |   || |     | ||| |                                                                
TACGATGAAGCTGAGAGGAGGAGGGAAATGGCTAAGAACTCGTTAGAGAGATATACACATTACTACGAGCGATGGGCCACGAACGAATCAgttgagtttccaatttgag------tatctga-taggcctttctaactt-cgctcatggtacag---------------------------------------------------------------

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|29681156|gb|CB677431.1|CB677431
EST:     CGCTTGAGAGATATACACACTATTATGAACGGTGGGCAGCCAATCAGTCG                         TCGAGGCAAAAGGCATTAGGAGATCTGCTGAGTTTGCAAAACGACAAG
genomic: CGCTTGAGAGATATACACACTATTATGAACGGTGGGCAGCCAATCAGTCGgtaagttatt ... cgttatgcagTCGAGGCAAAAGGCATTAGGAGATCTGCTGAGTTTGCAAAACGACAAG